4YPM

Crystal structure of a LonA protease domain in complex with bortezomib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.52950.2 M sodium citrate pH 6.5 and 10 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.3963.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.343α = 90
b = 122.343β = 90
c = 103.125γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDRAYONIX MX325HE2014-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A10.8NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.85201000.1133.4421.739226392252
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.921004.629

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.8519.8537301192499.80.178350.177140.20094RANDOM22.072
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.1-0.05-0.10.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.246
r_dihedral_angle_4_deg19.296
r_dihedral_angle_3_deg13.703
r_long_range_B_refined5.468
r_dihedral_angle_1_deg5.279
r_long_range_B_other5.109
r_scangle_other3.256
r_scbond_it2.021
r_scbond_other2.014
r_mcangle_other2.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.246
r_dihedral_angle_4_deg19.296
r_dihedral_angle_3_deg13.703
r_long_range_B_refined5.468
r_dihedral_angle_1_deg5.279
r_long_range_B_other5.109
r_scangle_other3.256
r_scbond_it2.021
r_scbond_other2.014
r_mcangle_other2.013
r_mcangle_it2.012
r_angle_refined_deg1.386
r_mcbond_it1.265
r_mcbond_other1.26
r_angle_other_deg0.805
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2213
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
Cootmodel building